Variant report

Variant	rs10799573
Chromosome Location	chr1:224625075-224625076
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224624808..224626574-chr1:224690723..224692820,2	K562	blood:
2	chr1:224606906..224609708-chr1:224624793..224626933,3	MCF-7	breast:
3	chr1:224617651..224619446-chr1:224625035..224626931,2	MCF-7	breast:
4	chr1:224620020..224622844-chr1:224624641..224626201,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143786	Chromatin interaction
ENSG00000162923	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10127813	0.88[MEX][hapmap]
rs10495220	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10753465	0.88[MEX][hapmap]
rs10799574	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916610	0.82[AMR][1000 genomes]
rs10916616	0.88[MEX][hapmap]
rs1112556	0.85[ASN][1000 genomes]
rs11801436	0.82[MEX][hapmap]
rs12124686	1.00[CHB][hapmap]
rs12128292	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12140423	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12354311	0.90[EUR][1000 genomes]
rs12745610	0.81[MEX][hapmap]
rs12755816	0.82[MEX][hapmap]
rs1361618	0.85[ASN][1000 genomes]
rs1539207	0.88[MEX][hapmap]
rs1572992	0.80[ASN][1000 genomes]
rs2405023	0.85[ASN][1000 genomes]
rs4653588	0.85[ASN][1000 genomes]
rs4654037	0.88[MEX][hapmap]
rs56168737	0.85[ASN][1000 genomes]
rs6426123	0.88[MEX][hapmap]
rs6426126	0.82[MEX][hapmap]
rs6673865	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693653	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7517754	0.88[MEX][hapmap]
rs7522956	0.82[MEX][hapmap]
rs7536124	0.85[ASN][1000 genomes]
rs7542507	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1013149	chr1:224605943-224646382	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv535312	chr1:224605943-224646382	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10799573	CNIH4	cis	Esophagus Muscularis	GTEx
rs10799573	CNIH4	cis	Muscle Skeletal	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224623200-224626200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:224623200-224634800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:224623200-224644400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:224623400-224625200	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr1:224623400-224626400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:224623400-224626800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:224623400-224626800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:224623400-224628200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:224623400-224631600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:224623400-224633400	Weak transcription	Gastric	stomach
11	chr1:224623400-224634600	Weak transcription	Lung	lung
12	chr1:224623400-224634800	Weak transcription	Aorta	Aorta
13	chr1:224623400-224634800	Weak transcription	Left Ventricle	heart
14	chr1:224623400-224634800	Weak transcription	Ovary	ovary
15	chr1:224623400-224634800	Weak transcription	Right Atrium	heart
16	chr1:224623400-224638000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:224623400-224641000	Weak transcription	Fetal Intestine Large	intestine
18	chr1:224623400-224643000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:224623400-224644600	Weak transcription	Right Ventricle	heart
20	chr1:224623600-224625200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr1:224623600-224625200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:224623600-224625400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:224623600-224626800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:224623600-224627800	Weak transcription	Fetal Brain Female	brain
25	chr1:224623600-224627800	Weak transcription	Fetal Stomach	stomach
26	chr1:224623600-224628000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:224623600-224628800	Weak transcription	Brain Germinal Matrix	brain
28	chr1:224623600-224629800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:224623600-224630400	Weak transcription	Fetal Brain Male	brain
30	chr1:224623600-224635000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:224623600-224635600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:224623600-224636200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:224623600-224637400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:224623600-224642200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:224623600-224644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:224623600-224644600	Weak transcription	Brain Substantia Nigra	brain
37	chr1:224623800-224625200	Enhancers	HepG2	liver
38	chr1:224623800-224626600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:224623800-224630200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:224623800-224632600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:224623800-224634800	Weak transcription	Stomach Mucosa	stomach
42	chr1:224623800-224635000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr1:224623800-224644400	Weak transcription	Brain Anterior Caudate	brain
44	chr1:224624000-224625200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:224624000-224625200	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr1:224624000-224625200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr1:224624000-224625400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:224624000-224625400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:224624000-224626400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:224624000-224626400	Weak transcription	Placenta	Placenta

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